1. Field of the Invention
The present invention relates to the field of microarray analysis. More particularly, the present invention concerns methods, compositions and apparatus relating to translucent, solid, two-dimensional (2D) matrix assay devices for microarray analysis. In certain embodiments of the invention, the microarray may be a reconfigurable microarray.
2. Description of Related Art
Microarray analysis involves the attachment of capture molecules, such as antibodies or oligonucleotides, to a solid matrix. Typically, the array is designed so that capture molecules specific for particular target analytes are attached to identifiable locations on the matrix. After exposure to a sample suspected of containing one or more target analytes, the matrix is analyzed to determine if substances in the sample bind to the capture molecules at one or more locations on the array.
Two-dimensional microarrays have proven useful for a wide range of applications, such as genomic research. Arrays of oligonucleotide probes may be used to determine the match or mismatch for a given sample of DNA or RNA, as in the detection of disease-associated single nucleotide polymorphisms (SNPs). Gene expression-profiling with microarrays containing probes against target gene mRNAs has been used to identify genes that are up- or down-regulated in response to disease, drug treatment, developmental stage and other conditions. Microarrays have also been of use for applications in protein research. However, proteins are more difficult to attach to a solid matrix and far more complex than oligonucleotides. Thus, techniques for use with protein (antibody) microarrays often require modifications compared to the more simple nucleic acid microarrays. (See, e.g., Constans, The Scientist, 16:28, 2002.)
Many clinical diagnostic devices have been built around microarray platforms incorporating an appropriate solid matrix. These often contain capture molecules that have been printed or otherwise permanently affixed to the matrix. One of the problems with such fixed arrays is that they are static. Once an array has been printed, it cannot be changed or adapted to conduct any tests other than the ones that it was originally designed for. A reconfigurable microarray would be very advantageous in allowing flexibility of use.
Existing microarrays face additional problems. For example, the type of solid matrix used may affect the results obtained, depending on the method of analysis and the materials used. Most microarrays are produced using covalent, electrostatic or hydrophobic binding to attach capture probes to the surface of a solid matrix. The capture probes remain attached to the surface during sample analysis. Bound target molecules may be detected in a variety of ways. Most commonly, one or more fluorophore tags are attached to the target molecules or cells that are to be bound by a capture molecule. Once binding is complete the tags may be spectrophotometrically detected. Scanners, CCD cameras or similar detectors may be used to determine the location and signal intensity of fluorescent tags bound to matrix arrays.
The amount of probe material that can be affixed on a matrix surface depends on the composition of the solid matrix. If insufficient amounts of probe are affixed to the matrix, the resulting fluorescent signal will be so weak that it cannot be detected even if the probe captures a tagged target molecule. It is also not sufficient to bind high concentrations of probe molecules to the surface of a solid matrix, if the matrix does not provide sufficient conformational or steric freedom to allow probes to bind to target molecules.
The solid matrix must also preserve the functional activity of the probe. Proteins, such as antibodies, attached to a solid matrix may undergo denaturation over time, rendering antibodies inactive or enzymes dysfunctional. In such cases, the signal strength (and the amount of target protein identified in a sample) may vary by the length of time following matrix array manufacture. Although such time-dependent processes may be compensated for in part by the use of external standard proteins, the denaturation rates for different antibodies or enzymes affixed to the same matrix may not be identical.
Other characteristics of the solid matrix used for 2D arrays may also be important. For example, the opacity of the solid matrix may render it useless for certain kinds of analysis. Opaque materials only allow sample analysis to occur on the same side of the solid matrix as the probe array. This prevents the use of see-through optics that detect light from the opposite side of the matrix. For example, a matrix array may be opposed to a fluidic cube or other fluidic device, with probe molecules attached to the array within a cavity formed by the fluidics cube. Detection of real-time binding of target molecules to the probes would be greatly facilitated if emitted light could be detected from the opposite surface of the array. This is not feasible if the array is opaque to the emitted light.
A need exists for a translucent solid matrix that could be used with a fluidic cube or other flow device. Such translucent matrix materials should also allow for binding of high concentrations of probe molecules, while maintaining probe molecules in an active state.